/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.*;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.util.List;
public class IdCanvas extends Panel
{
boolean fastPaint = false;
- java.util.Vector searchResults;
+ List<SequenceI> searchResults;
public IdCanvas(AlignViewport av)
{
PaintRefresher.Register(this, av.getSequenceSetId());
}
- public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
- int ypos)
+ public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
+ int i, int starty, int ypos)
{
int charHeight = av.getCharHeight();
((i - starty) * charHeight) + ypos + charHeight
- (charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (hiddenRows)
{
drawMarker(i, starty, ypos);
}
return;
}
- gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical
- * av.charHeight);
+ gg.copyArea(0, 0, getSize().width, imgHeight, 0,
+ -vertical * av.getCharHeight());
int ss = av.startSeq, es = av.endSeq, transY = 0;
if (vertical > 0) // scroll down
}
else
{
- transY = imgHeight - vertical * av.charHeight;
+ transY = imgHeight - vertical * av.getCharHeight();
}
}
else if (vertical < 0)
}
imgHeight = getSize().height;
- imgHeight -= imgHeight % av.charHeight;
+ imgHeight -= imgHeight % av.getCharHeight();
if (imgHeight < 1)
{
g.drawImage(image, 0, 0, this);
}
+ /**
+ * local copy of av.getCharHeight set at top of drawIds
+ */
+ private int avcharHeight;
+
void drawIds(int starty, int endy)
{
+ // hardwired italic IDs in applet currently
Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
.getFont().getSize());
+ // temp variable for speed
+ avcharHeight = av.getCharHeight();
gg.setFont(italic);
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
+ && av.getShowHiddenMarkers();
+
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
int annotationHeight = 0;
AnnotationLabels labels = null;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
AnnotationPanel ap = new AnnotationPanel(av);
annotationHeight = ap.adjustPanelHeight();
labels = new AnnotationLabels(av);
}
-
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = avcharHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += avcharHeight;
}
- int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+ int cHeight = alheight * avcharHeight + hgap + annotationHeight;
int rowSize = av.getEndRes() - av.getStartRes();
-
// Draw the rest of the panels
for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
&& (row < maxwidth); ypos += cHeight, row += rowSize)
for (int i = starty; i < alheight; i++)
{
- SequenceI s = av.alignment.getSequenceAt(i);
+ SequenceI s = av.getAlignment().getSequenceAt(i);
gg.setFont(italic);
- if (av.hasHiddenRows)
+ if (doHiddenCheck)
{
setHiddenFont(s);
}
- drawIdString(gg, s, i, 0, ypos);
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
}
if (labels != null)
{
- gg.translate(0, ypos + (alheight * av.charHeight));
+ gg.translate(0, ypos + (alheight * avcharHeight));
labels.drawComponent(gg, getSize().width);
- gg.translate(0, -ypos - (alheight * av.charHeight));
+ gg.translate(0, -ypos - (alheight * avcharHeight));
}
}
for (int i = starty; i < endy; i++)
{
- seq = av.alignment.getSequenceAt(i);
+ seq = av.getAlignment().getSequenceAt(i);
if (seq == null)
{
continue;
}
gg.setFont(italic);
// boolean isrep=false;
- if (av.hasHiddenRows)
+ if (doHiddenCheck)
{
// isrep =
setHiddenFont(seq);
gg.setColor(currentColor);
// TODO: isrep could be used to highlight the representative in a
// different way
- gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,
- av.charHeight);
+ gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
+ avcharHeight);
gg.setColor(currentTextColor);
gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
- (((i - starty) * av.charHeight) + av.charHeight)
- - (av.charHeight / 5));
+ (((i - starty) * avcharHeight) + avcharHeight)
+ - (avcharHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (hiddenRows)
{
drawMarker(i, starty, 0);
}
}
}
- public void setHighlighted(java.util.Vector found)
+ public void setHighlighted(List<SequenceI> list)
{
- searchResults = found;
+ searchResults = list;
repaint();
}
void drawMarker(int i, int starty, int yoffset)
{
- SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+ SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
// Use this method here instead of calling hiddenSeq adjust
// 3 times.
int hSize = hseqs.length;
gg.setColor(Color.blue);
if (below)
{
- gg.fillPolygon(new int[]
- { getSize().width - av.charHeight, getSize().width - av.charHeight,
- getSize().width }, new int[]
- { (i - starty) * av.charHeight + yoffset,
- (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
- (i - starty) * av.charHeight + yoffset }, 3);
+ gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width }, new int[] {
+ (i - starty) * avcharHeight + yoffset,
+ (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
+ (i - starty) * avcharHeight + yoffset }, 3);
}
if (above)
{
- gg.fillPolygon(new int[]
- { getSize().width - av.charHeight, getSize().width - av.charHeight,
- getSize().width }, new int[]
- { (i - starty + 1) * av.charHeight + yoffset,
- (i - starty + 1) * av.charHeight + yoffset - av.charHeight / 4,
- (i - starty + 1) * av.charHeight + yoffset }, 3);
+ gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width }, new int[] {
+ (i - starty + 1) * avcharHeight + yoffset,
+ (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
+ (i - starty + 1) * avcharHeight + yoffset }, 3);
}
}
Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
.getSize());
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
gg.setFont(bold);
return true;
git://source.jalview.org / jalview.git / blobdiff